Car in question: Manual 99 Jetta VR6 (119000 mi)

The story:

The past few days have been exceptionally warm, around 25 degrees celsius, a tad hire at times. My car has been fine on cold start, and after a 1 hour highway drive on Tuesday, I noticed the car bucking a little while giving it throttle on the freeway. Upon arriving to my friend's house, there is a bigger bump which you're forced into going over in the road and my car completely shut off AFTER GOING INTO NEUTRAL TO SLOW DOWN, CEL was thrown for fuel pump relay. I replaced the relay with a confirmed working unit and because I didn't scan first, also changed the fuel pump with a confirmed working unit. Topped her off with gas and all was dandy.

Drove the next (city driving), and wasn't having any issues, until 2 minutes from home, car stalls out when I WENT IN NEUTRAL to brake for a red light. Cranked 3 times and spark, fuel and compression were there but car wouldn't fire up, so I pumped the throttle while turning, and voila, fired up, made it home.

Driving yesterday (at full operating temperature, I go to shift from 4th to 5th at about 2400 rpms and the car attempts to stall out. I clutch kick and blimp the throttle and all is good, however, once again, intermittent hesitation while driving in gear (super short jolt when on throttle).

Last night coming home from work, my OEM radio (not Bose unit, just Premium Audio unit) was working. When firing the car up after it sat for an hour, the radio would not turn on. The red anti-theft light keeps blinking while the car is on, and gets power (lights up when lightswitch is turned.

What I want to know is:

The stalling issue - is it a) coil pack or crank position sensor that's causing the stalling issues?

b) why will the radio not turn on (NO SAFE is displayed on unit, and popped fuse 22 out for 2 minutes and plugged it back and disconnected the battery as well and reconnected).

c) I use my key FOB to arm my alarm, but my MFA has not reset in over 6 hours travelling time now.

are b) and c) possibly linked to a faulty ignition switch?

Please help, this is my daily car, and with work and school, I try my best to maintain this car.

Thanks.